Chlorine in PDB 5dj1: Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme

The structure of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme, PDB code: 5dj1 was solved by N.R.Silvaggi, L.Han, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.45 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.718, 108.277, 195.412, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 17.1

The structure of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme (pdb code 5dj1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme, PDB code: 5dj1:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl500 b:27.5 occ:1.00 HH12 A:ARG352 2.3 24.1 1.0 HH22 A:ARG352 2.5 24.1 1.0 HD21 A:ASN160 2.6 21.5 1.0 HA3 A:GLY28 2.8 29.6 1.0 HE3 A:LLP221 2.9 31.1 1.0 H A:GLY28 3.0 28.0 1.0 NH1 A:ARG352 3.1 20.1 1.0 NH2 A:ARG352 3.2 20.1 1.0 HE1 A:PHE115 3.3 36.6 1.0 ND2 A:ASN160 3.4 17.9 1.0 CZ A:ARG352 3.6 21.7 1.0 N A:GLY28 3.6 23.4 1.0 CA A:GLY28 3.6 24.7 1.0 HD22 A:ASN160 3.7 21.5 1.0 CE A:LLP221 3.8 25.9 1.0 HH11 A:ARG352 3.8 24.1 1.0 NZ A:LLP221 3.8 24.1 1.0 HH21 A:ARG352 3.9 24.1 1.0 CE1 A:PHE115 3.9 30.5 1.0 HD1 A:PHE115 4.0 32.8 1.0 HA2 A:GLY28 4.1 29.6 1.0 HG11 A:VAL309 4.2 30.1 1.0 HD3 A:LLP221 4.3 30.7 1.0 CD1 A:PHE115 4.3 27.4 1.0 O3 A:LLP221 4.4 21.3 1.0 CG A:ASN160 4.5 17.3 1.0 HE2 A:LLP221 4.5 31.1 1.0 C4' A:LLP221 4.6 20.5 1.0 HZ A:PHE191 4.6 34.0 1.0 OD1 A:ASN160 4.7 12.9 1.0 CD A:LLP221 4.7 25.6 1.0 HA A:ASP27 4.7 37.0 1.0 C A:GLY28 4.7 21.7 1.0 OD1 A:ASP27 4.7 64.7 1.0 HE1 A:PHE339 4.8 21.0 1.0 C A:ASP27 4.8 25.1 1.0 NE A:ARG352 4.9 23.6 1.0 CZ A:PHE115 4.9 27.7 1.0

Chlorine binding site 2 out of 4 in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl500 b:33.7 occ:1.00 HH12 B:ARG352 2.5 23.5 1.0 HH22 B:ARG352 2.6 25.2 1.0 H B:GLY28 2.8 32.7 1.0 HD21 B:ASN160 2.8 30.4 1.0 HA3 B:GLY28 3.1 32.2 1.0 HE3 B:LLP221 3.1 35.7 1.0 HE1 B:PHE115 3.2 68.1 1.0 NH1 B:ARG352 3.3 19.6 1.0 NH2 B:ARG352 3.3 21.0 1.0 N B:GLY28 3.5 27.2 1.0 ND2 B:ASN160 3.6 25.4 1.0 CA B:GLY28 3.7 26.9 1.0 CZ B:ARG352 3.8 26.4 1.0 HD22 B:ASN160 3.9 30.4 1.0 CE1 B:PHE115 3.9 56.7 1.0 CE B:LLP221 4.0 29.8 1.0 NZ B:LLP221 4.0 27.6 1.0 HH11 B:ARG352 4.0 23.5 1.0 HH21 B:ARG352 4.0 25.2 1.0 HD1 B:PHE115 4.1 62.0 1.0 HA2 B:GLY28 4.3 32.2 1.0 HA B:ASP27 4.3 36.3 1.0 O3 B:LLP221 4.3 27.0 1.0 HG11 B:VAL309 4.4 27.4 1.0 CD1 B:PHE115 4.4 51.6 1.0 HE2 B:LLP221 4.6 35.7 1.0 OD1 B:ASP27 4.6 68.7 1.0 C4' B:LLP221 4.6 27.2 1.0 C B:ASP27 4.7 35.8 1.0 CG B:ASN160 4.7 25.8 1.0 HD3 B:LLP221 4.8 37.2 1.0 C B:GLY28 4.9 26.4 1.0 OD1 B:ASN160 4.9 19.1 1.0 HZ B:PHE191 4.9 43.3 1.0 HE1 B:PHE339 4.9 39.6 1.0 CZ B:PHE115 5.0 49.4 1.0 H B:HIS29 5.0 31.6 1.0 CA B:ASP27 5.0 30.2 1.0

Chlorine binding site 3 out of 4 in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl500 b:33.2 occ:1.00 HH12 C:ARG352 2.5 26.7 1.0 HH22 C:ARG352 2.5 26.8 1.0 HD21 C:ASN160 2.7 27.4 1.0 H C:GLY28 2.9 32.2 1.0 HA3 C:GLY28 2.9 31.1 1.0 HE3 C:LLP221 3.0 34.7 1.0 HE1 C:PHE115 3.1 56.8 1.0 NH1 C:ARG352 3.2 22.2 1.0 NH2 C:ARG352 3.2 22.3 1.0 N C:GLY28 3.5 26.8 1.0 ND2 C:ASN160 3.5 22.8 1.0 CA C:GLY28 3.7 25.9 1.0 CZ C:ARG352 3.7 27.0 1.0 NZ C:LLP221 3.8 28.5 1.0 CE1 C:PHE115 3.8 47.3 1.0 CE C:LLP221 3.8 28.9 1.0 HD22 C:ASN160 3.8 27.4 1.0 HH11 C:ARG352 3.9 26.7 1.0 HH21 C:ARG352 3.9 26.8 1.0 HD1 C:PHE115 4.0 50.1 1.0 HA2 C:GLY28 4.2 31.1 1.0 HG11 C:VAL309 4.2 24.3 1.0 CD1 C:PHE115 4.2 41.8 1.0 O3 C:LLP221 4.3 27.4 1.0 HD3 C:LLP221 4.5 35.2 1.0 HA C:ASP27 4.5 44.5 1.0 HE2 C:LLP221 4.5 34.7 1.0 C4' C:LLP221 4.5 27.3 1.0 CG C:ASN160 4.6 25.6 1.0 HZ C:PHE191 4.7 45.2 1.0 C C:ASP27 4.7 29.4 1.0 OD1 C:ASN160 4.7 21.6 1.0 C C:GLY28 4.8 28.7 1.0 CZ C:PHE115 4.8 45.5 1.0 OD1 C:ASP27 4.8 71.2 1.0 CD C:LLP221 4.8 29.4 1.0 HZ C:PHE115 4.9 54.5 1.0 NE C:ARG352 5.0 23.7 1.0

Chlorine binding site 4 out of 4 in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl500 b:27.4 occ:1.00 HH12 D:ARG352 2.3 23.8 1.0 HH22 D:ARG352 2.4 24.9 1.0 HD21 D:ASN160 2.7 28.1 1.0 HA3 D:GLY28 2.7 26.8 1.0 HE3 D:LLP221 2.9 32.9 1.0 NH1 D:ARG352 3.1 19.8 1.0 H D:GLY28 3.1 25.0 1.0 NH2 D:ARG352 3.2 20.7 1.0 HE1 D:PHE115 3.2 30.9 1.0 ND2 D:ASN160 3.5 23.4 1.0 CA D:GLY28 3.5 22.3 1.0 CZ D:ARG352 3.6 21.7 1.0 N D:GLY28 3.6 20.8 1.0 NZ D:LLP221 3.7 24.8 1.0 CE D:LLP221 3.7 27.4 1.0 HH11 D:ARG352 3.8 23.8 1.0 HD22 D:ASN160 3.8 28.1 1.0 HH21 D:ARG352 3.9 24.9 1.0 CE1 D:PHE115 3.9 25.7 1.0 HA2 D:GLY28 4.0 26.8 1.0 HD1 D:PHE115 4.0 32.9 1.0 HG11 D:VAL309 4.1 19.7 1.0 HD3 D:LLP221 4.2 31.7 1.0 CD1 D:PHE115 4.4 27.4 1.0 O3 D:LLP221 4.4 24.7 1.0 C4' D:LLP221 4.4 25.6 1.0 HZ D:PHE191 4.4 29.3 1.0 HE2 D:LLP221 4.5 32.9 1.0 CG D:ASN160 4.5 19.2 1.0 CD D:LLP221 4.6 26.4 1.0 C D:GLY28 4.6 25.0 1.0 OD1 D:ASN160 4.7 20.9 1.0 NE D:ARG352 4.9 18.6 1.0 C D:ASP27 4.9 22.3 1.0 HA D:ASP27 4.9 40.8 1.0 H4'1 D:LLP221 4.9 30.7 1.0 CG1 D:VAL309 5.0 16.4 1.0 CZ D:PHE115 5.0 23.0 1.0

L.Han, A.W.Schwabacher, G.R.Moran, N.R.Silvaggi. Streptomyces Wadayamensis Mppp Is A Pyridoxal 5'-Phosphate-Dependent L-Arginine Alpha-Deaminase, Gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry V. 54 7029 2015.
ISSN: ISSN 0006-2960
PubMed: 26551990
DOI: 10.1021/ACS.BIOCHEM.5B01016